3FWP | pdb_00003fwp

X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution

PDB DOI: https://doi.org/10.2210/pdb3FWP/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-19 Released: 2010-01-19
Deposition Author(s): Lashkov, S.A., Mikhailov, A.M., Gabdulkhakov, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.206 (Depositor), 0.192 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution.

Lashkov, A.A., Zhukhlistova, N.E., Gabdoulkhakov, A.H., Shtil, A.A., Efremov, R.G., Betzel, C., Mikhailov, A.M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 51-60

PubMed: 20057049 Search on PubMed
DOI: https://doi.org/10.1107/S0907444909044175
Primary Citation Related Structures:
3FWP

PubMed Abstract:
Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure of Salmonella typhimurium uridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2'-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 A resolution (R(cryst) = 17.6%, R(free) = 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2'-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI.

Organizational Affiliation

A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Prospect, 119333 Moscow, Russia.

Macromolecule Content

Total Structure Weight: 164.1 kDa
Atom Count: 12,046
Modeled Residue Count: 1,454
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: STM3968, STMD1.21, udp EC: 2.4.2.3
UniProt
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1F6 Go to UniProtKB: P0A1F6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A1F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANU Query on ANU Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] SDF format, chain O [auth F] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] MOL2 format, chain O [auth F] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D] mmCIF format, chain O [auth F]	I [auth B], L [auth D], O [auth F]	2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil C₉ H₁₀ N₂ O₅ UUGITDASWNOAGG-CCXZUQQUSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth F] Interactions & Density Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain N [auth F] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain N [auth F] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain N [auth F]	G [auth B], K [auth D], N [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth B] Focus chain K [auth D] Focus chain N [auth F] Interactions & Density Focus chain G [auth B] Focus chain K [auth D] Focus chain N [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth F] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth F] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth F]	H [auth B], J [auth C], M [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth F] Interactions & Density Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.206 (Depositor), 0.192 (DCC)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 124.07	β = 90
c = 134.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Lashkov, S.A.

Mikhailov, A.M.

Gabdulkhakov, A.G.

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description